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When "regular" items, such as list items, documents, or libraries or lists, get deleted from a SharePoint site, they go to the end user (aka first stage) recycle bin, and their size continues to count against the quota. If they are deleted from the end user recycle bin (or if they are auto-deleted after 30 days), then they stop counting against the quota. This can be verified on the "Site Collection Quotas and Locks" page in Central Admin.

When a site (not site collection) gets deleted, it skips the first stage recycle bin and goes straight to the 2nd stage recycle bin. However, its size appears to continue counting against the site quota. (Again, verified in Central Admin.)

Will the site size continue to count against the quota until it is removed from the second stage recycle bin, either by manual removal or auto-removal after thirty days, or will a timer job reduce the reported usage?

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If a site is deleted, it will skip the 1st stage recycle bin and go straight to the 2nd.and still counted towards the quota. this is expected behaviour.

It will be gone either after 30 days( as your settings) or reach 50% of your site live quota.

If you want, you can reduce the 50% number to down to get the space back quikcly or delete it manually.

This is from Office article:

NOTE: Deleted sites are automatically sent to the Second-Stage Recycle Bin and can be restored only by a Site Collection Administrator. https://support.office.com/en-us/article/Manage-the-Recycle-Bin-of-a-SharePoint-Online-site-collection-5fa924ee-16d7-487b-9a0a-021b9062d14b

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  • Thanks for the response. That's what I figured. Do you know if this information is available oon technet or msdn in something other than the forums?
    – Chloraphil
    May 6, 2016 at 20:24
  • I don't think, i saw this on TechNet but it is from my experience but I will try to o search if found will update.
    – Waqas Sarwar MVP
    May 6, 2016 at 20:25
  • check my updated answer...
    – Waqas Sarwar MVP
    May 6, 2016 at 20:28
  • Thanks, but this article says that items in the 2nd stage recycle bin don't count against the quota, and does not mention an exception for sites. Still, thank you!
    – Chloraphil
    May 6, 2016 at 20:31

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